Limitations

Only has HTML output at the moment

Limited detection of input formats

Problems with PATH

To find the pandoc executable, ideally Atom should be able to find it on your PATH. Unfortunately, environment variables are a bit of an issue with GUI applications on OS X. Google it or see Setting Environment Variables in OS X?.

For the atom command, you need to make sure Atom is loaded via env (in some older versions of Atom it is not).